Hello. Can someone help me with drawing hydrogen bonds among different molecules, with an example below? I understood how water molecules are linked to each other by hydrogen bonds. But I have a problem drawing these bonds in other biomolecules. Thanks!

1 Answer
Jul 3, 2015

Answer:

Here's what you must look for in order to be able to draw hydrogen bonds.

Explanation:

As you know, hydrogen bonds are a special case of dipole-dipole interactions in which you have a hydrogen atom bonded to one of the three most electronegative atoms in the periodic table: fluorine, oxygen, or nitrogen.

In essence, a hydrogen bond is formed when the partial positive charge that appears on the hydrogen atom of one molecule is attracted to a lone pair of electrons located on another molecule.

This is why each water molecule can form hydrogen bonds to 4 other water molecules.

So, if you are looking to draw a hydrogen bond between two molecules, look for two things

  • hydrogen atoms attached to fluorine, oxygen, or nitrogen on one molecule;
  • lone pairs of electrons on another molecule.

Here are some examples of how hydrogen bonds are formed between various molecules and water

http://www.bio.miami.edu/tom/courses/bil255/bil255goods/02_bonds.html

Here are how hydrogen bonds are formed between side chains in proteins (left side of the image)

https://www.studyblue.com/notes/note/n/cell-bi314-study-guide-2014-15-ri/deck/14085828

The hydrogen bond is formed between the partial positive hydrogen atom of the side chain and a lone pair of electrons present on the oxygen atom of carboxyl group.

Likewise, a similar partial positive hydrogen can form a hydrogen bond with the lone pair of electrons present on the nitrogen atom of an amine.

So, as a conclusion, always look for partial positive hydrogen atoms (bonded to fluorine, oxygen, or nitrogen) and lone pairs of electrons, and draw hydrogen bonds using dotted lines, #"- - - - -"#.